R help - Sep 2009 - read.delim very slow in reading files with lots of columns

Hi,

 

I am trying to read a tab-delimited file into R (Ver. 2.8). The machine I am
using is 64bit Linux with 16 GB.

The file is basically a matrix(~600x700000) and as large as 3GB.

 

The read.delim() ran extremely slow (hours) even with a subset of the file (31
MB with 6x700000)

I monitored the memory usage, and found it constantly only took less than 1% of
16GB memory.

Does read.delim() have difficulty to read files with lots of columns?

Any suggestions?

 

Thanks,

Mike

 


	[[alternative HTML version deleted]]

use the 'colClasses' argument and you can also set 'nrows'.

b

On Sep 23, 2009, at 8:24 PM, Ping-Hsun Hsieh wrote:
> Hi,
>
>
>
> I am trying to read a tab-delimited file into R (Ver. 2.8). The  
> machine I am using is 64bit Linux with 16 GB.
>
> The file is basically a matrix(~600x700000) and as large as 3GB.
>
>
>
> The read.delim() ran extremely slow (hours) even with a subset of  
> the file (31 MB with 6x700000)
>
> I monitored the memory usage, and found it constantly only took less  
> than 1% of 16GB memory.
>
> Does read.delim() have difficulty to read files with lots of columns?
>
> Any suggestions?
>
>
>
> Thanks,
>
> Mike
>
>
>
>
>        [[alternative HTML version deleted]]
>
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